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The Pfam protein families database: embracing AI/ML.
Paysan-Lafosse T, Andreeva A, Blum M, Chuguransky SR, Grego T, Pinto BL, Salazar GA, Bileschi ML, Llinares-López F, Meng-Papaxanthos L, Colwell LJ, Grishin NV, Schaeffer RD, Clementel D, Tosatto SCE, Sonhammer E, Wood V, Bateman A. Paysan-Lafosse T, et al. Among authors: schaeffer rd. Nucleic Acids Res. 2024 Nov 14:gkae997. doi: 10.1093/nar/gkae997. Online ahead of print. Nucleic Acids Res. 2024. PMID: 39540428
ECOD: an evolutionary classification of protein domains.
Cheng H, Schaeffer RD, Liao Y, Kinch LN, Pei J, Shi S, Kim BH, Grishin NV. Cheng H, et al. Among authors: schaeffer rd. PLoS Comput Biol. 2014 Dec 4;10(12):e1003926. doi: 10.1371/journal.pcbi.1003926. eCollection 2014 Dec. PLoS Comput Biol. 2014. PMID: 25474468 Free PMC article.
Manual classification strategies in the ECOD database.
Cheng H, Liao Y, Schaeffer RD, Grishin NV. Cheng H, et al. Among authors: schaeffer rd. Proteins. 2015 Jul;83(7):1238-51. doi: 10.1002/prot.24818. Epub 2015 May 8. Proteins. 2015. PMID: 25917548 Free PMC article.
A sequence family database built on ECOD structural domains.
Liao Y, Schaeffer RD, Pei J, Grishin NV. Liao Y, et al. Among authors: schaeffer rd. Bioinformatics. 2018 Sep 1;34(17):2997-3003. doi: 10.1093/bioinformatics/bty214. Bioinformatics. 2018. PMID: 29659718 Free PMC article.
34 results